At the urging of President Obama, Israeli Prime Minister Benjamin Netanyahu apologized to Turkey on Friday for the deaths of eight of its citizens during a raid in 2010 on a Gaza flotilla.

In a 30-minute phone call with Turkey's Prime Minister Recep Tayyip Erdogan, Netanyahu acknowledged "operational mistakes" in the raid and said he "regretted" the incident had led to a deterioration of the two countries' relationship, according to a senior administration official who spoke on the condition of anonymity to describe the sensitive nature of the call.

Obama, who finished up a two-day visit to Israel on Friday, was by Netanyahu's side during the phone call, which he helped broker. The president joined the Turkish and Israeli leaders' conversation at the end of the call.

At a news conference in Jordan later on Friday, Obama said Israel and Turkey are working to restore relations but the call marked an important step in mending the relationship.

"I have long said that it is both in the interest of Israel and Turkey to restore normal relations between two countries that historically have had good ties," Obama said. "It broke down several years ago as a result of the flotilla incident. For the last two years, I have spoken to Prime Minister Netanyahu and Prime Minister Erdogan about why this rupture has to be mended — that they don't have to agree on everything in order for them to come together on a whole range of common interests and common concerns."

Obama said he broached with Netanyahu the possibility of a call with Erdogan during their private conversations this week, and Netanyahu agreed that the timing was right. The phone call was made from a trailer at the airport in Tel Aviv just before Obama departed for Jordan on Friday.

Erdogan accepted the apology. The phone call was described by one administration official as a "first step" toward normalizing relations between the two countries.

"There are obviously still going to be some significant disagreements between Turkey and Israel — not just on the Palestinian question but on a range of different issues," Obama said. "But they also have a whole range of shared interests, and they both happen to be extraordinarily strong partners and friends of ours."

Nine pro-Palestinian activists — eight Turkish citizens and one American — were killed aboard the Turkish-flagged ship on May 31, 2010, after passengers resisted a takeover by Israeli naval commandos. The flotilla was en route to Gaza as part of a campaign to bring attention to Israel's blockade of the Palestinian territory.

The flotilla incident did significant damage to the Israel-Turkey relationship. The countries once had close ties, but Turkey withdrew its ambassador from Israel after the incident.

The warming of the relations comes as two countries grapple with the crisis in Syria, where the 2-year-old civil war has ground to a stalemate.

Turkey has been overwhelmed by Syrian refugees fleeing the crisis. Netanyahu has expressed alarm about Syria's significant chemical weapons arsenal getting into the hands of extremists or Syria's President Bashar Assad deploying the weapons as he loses his grip on power.

Both countries are also concerned about Iran's nuclear program.

"Both Israel and Turkey find the notion of an Iran possessing nuclear weapons wholly unacceptable, " said Guy Ziv, a professor at American University 's international service school and an expert on U.S.-Israel relations. "In the immediate, both countries are extremely concerned about the spillover effect of the Syrian civil war."

The apology was easier for Netanyahu to make with the sidelining of former Israel foreign minister Avigdor Lieberman, Ziv said. Lieberman had refused to allow an apology, but he resigned from his powerful post late last year as he faced charges of fraud and breach of trust.

President Obama tours Jordan's ancient city of Petra on March 23. (Photo: Pablo Martinez Monsivais, AP)

U.S. security personnel patrol the ancient city of Petra, Jordan, ahead of the arrival of President Obama. Obama toured the fabled city on Saturday, described the landscape of soaring red rock cliffs as "amazing." (Photo: Mohammad Hannon, AP)

Israeli President Shimon Peres, left, watches as President Obama shakes hands with Israeli Prime Minister Benjamin Netanyahu at Ben Gurion International Airport. Obama concluded his first visit to Israel and the West Bank after three-days of meetings with Israeli and Palestinian leaders. (Photo: Lior Mizrahi, Getty Images)

Israeli President Shimon Peres, left, President Obama and Israeli Prime Minister Benjamin Netanyahu observe a moment of silence in the Hall of Remembrance at the Yad Vashem Holocaust Museum in Jerusalem. The museum is a memorial to the six million Jews killed by the Nazis during World War II. (Photo: Saul Loeb, AFP/Getty Images)

Israeli Prime Minister Benjamin Netanyahu, left, President Obama and Israeli President Shimon Peres leave the grave of Theodore Herzl after a wreath laying ceremony at the Yad Vashem cemetery at Mount Herzl in Jerusalem. Herzl is the founder of the political form of Zionism. a movement that established a Jewish homeland in Palestine. (Photo: Kobi Gideon, GPO, via Getty Images)

Israelis shout slogans during a protest against President Obama's visit. The activists are demanding the release of Jonathan Pollard, a Jewish American who was convicted in 1987 on charges of spying for Israel. (Photo: Lior Mizrahi, Getty Images)

Relatives of Palestinians held in Israeli jails burn posters of President Obama during a protest against his visit at the Jabalyia refugee camp in the northern Gaza Strip. (Photo: Mahmud Hams, AFP/Getty Images)